U.S. patent application number 14/426553 was filed with the patent office on 2015-09-03 for in vitro genetic diagnostic of inherited neuromuscular disorders.
The applicant listed for this patent is CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE - CNRS, INSERM (INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE), UNIVERSITE D'AUX-MARSEILLE, UNIVERSITE MONTPELLIER I. Invention is credited to Valerie Allamand, David Atlan, Marc Bartoli, Christophe Beroud, Gisele Bonne, Patrice Bourgeois, Sebahattin Cirak, Mireille Cossee, Rafael De Cid, Martin Krahn, Nicolas Levy, Francesco Muntoni, Isabelle Richard, Pascal Soularue.
Application Number | 20150247196 14/426553 |
Document ID | / |
Family ID | 46826398 |
Filed Date | 2015-09-03 |
United States Patent
Application |
20150247196 |
Kind Code |
A1 |
Soularue; Pascal ; et
al. |
September 3, 2015 |
IN VITRO GENETIC DIAGNOSTIC OF INHERITED NEUROMUSCULAR
DISORDERS
Abstract
The present invention provides a method for determining all the
molecular causes of Inherited Neuromuscular Disorders comprising
determining a number of copy number variation(s), and/or
determining a number of point mutation(s) on a physiological sample
comprising a genome of a subject.
Inventors: |
Soularue; Pascal; (Evry,
FR) ; Atlan; David; (Blonay, CH) ; Allamand;
Valerie; (Paris, FR) ; Bartoli; Marc;
(Marseille, FR) ; Beroud; Christophe; (Marseille,
FR) ; Bonne; Gisele; (Paris, FR) ; Bourgeois;
Patrice; (Marseille, FR) ; Cirak; Sebahattin;
(Washington, DC) ; Cossee; Mireille; (Montpellier,
FR) ; De Cid; Rafael; (Badalona, ES) ; Krahn;
Martin; (Marseille, FR) ; Levy; Nicolas;
(Marseille, FR) ; Muntoni; Francesco; (London,
GB) ; Richard; Isabelle; (Corbeil, FR) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
INSERM (INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE
MEDICALE)
UNIVERSITE D'AUX-MARSEILLE
CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE - CNRS
UNIVERSITE MONTPELLIER I |
Paris
Marseille
Paris Cedex 16
Montpellier |
|
FR
FR
FR
FR |
|
|
Family ID: |
46826398 |
Appl. No.: |
14/426553 |
Filed: |
September 6, 2013 |
PCT Filed: |
September 6, 2013 |
PCT NO: |
PCT/EP2013/068510 |
371 Date: |
March 6, 2015 |
Current U.S.
Class: |
506/3 ;
506/9 |
Current CPC
Class: |
C12Q 1/6809 20130101;
C12Q 1/6827 20130101; C12Q 2600/16 20130101; C12Q 2600/112
20130101; C12Q 1/6883 20130101; C12Q 1/6827 20130101; C12Q 1/6874
20130101; C12Q 2600/156 20130101; C12Q 2537/16 20130101; C12Q
2539/115 20130101; C12Q 2539/115 20130101; C12Q 2537/16 20130101;
C12Q 1/6874 20130101 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Foreign Application Data
Date |
Code |
Application Number |
Sep 7, 2012 |
EP |
12306081.6 |
Claims
1. A method of identifying in vitro molecular causes of Inherited
Neuromuscular Disorders, comprising the following steps: (i)
providing a physiological sample comprising a genome of a subject,
and (ii) implementing on said sample at least one of Process A and
Process B, wherein Process A is determining a number of copy number
variation(s), with respect to a sample of a normal subject, on at
least 25 genes selected from the 31 genes of Group 1 in Table 1;
and Process B is determining a number of point mutation(s), with
respect to a sample of a normal subject, on at least 25 genes
selected from the 31 genes of Group 1 in Table 1.
2. The method according to claim 1, wherein said step (ii)
comprises only Process A.
3. The method according to claim 1, wherein said step (ii)
comprises only Process B.
4. The method according to claim 1, wherein said step (ii)
comprises Process A and Process B.
5. The method according to claim 1, wherein Process A or Process B
is, or Process A and Process B are carried out on all the 31 genes
of Group 1 in Table 1.
6. The method according to claim 1, wherein Process A or Process B
is, or Process A and Process B are carried out on all the 31 genes
of Group 1, and on at least 10 genes of Group 2 in Table 1.
7. The method according to claim 1, wherein Process A or Process B
is, or Process A and Process B are carried out on all the 31 genes
of Group 1, on all the 15 genes of Group 2, and on at least 5 genes
of Group 3 in Table 1.
8. The method according to claim 1, wherein Process A or Process B
is, or Process A and Process B are carried out on all the 31 genes
of Group 1, on all the 15 genes of Group 2, on all the 9 genes of
Group 3, and on at least 4 genes of Group 4 in Table 1.
9. The method according to claim 1, wherein Process A or Process B
is, or Process A and Process B are carried out on all the genes of
the Table hereunder: TABLE-US-00005 ACTA1 FKRP BAG3 DNAJB6 ANO5
FLNC DAG1 FKTN BIN1 GNE LAMP2 MYH2 CAPN LAMA2 LDB3 SGCB CAV3 LARGE
MTM1 SGCD COL6A1 LMNA NEB CHKB COL6A2 MYOT PABPN1 CNTN1 COL6A3
POMT1 PTRF ITGA7 DES POMT2 TNNT1 PLEC1 DMD RYR1 TPM2 TCAP DNM2 SGCG
TPM3 DYSF SGCA VCP FHL1 TTN CFL2
10. The method according to claim 1, wherein Process A is carried
out with a Device A comprising a set of probes for said genes.
11. The method according to claim 10, wherein said set of probes
for said Device A comprises: probes evenly spaced by about 50 bp
distance between two consecutive probes, which hybridize said gene
plus a region of about 2000 bp at the 5' and 3' terminal exons, and
backbone probes not evenly spaced by about 1000 bp distance between
two consecutive probes, which represent on average from 20 to 30%
of the total probes on said device.
12. The method according to claim 10, wherein said set of probes
are manufactured according to the following rules: probes cover
gene+/-2 kb up and downstream average probe density is 1/50 probes
are alternated on (+) and (-) strands with a tiling of 10 pb tiling
in exonic regions and intron-exon boundaries (150 bp upstream and
downstream of the exon) 30 pb tiling in 3' and 5' UTR one probe for
100 bp in introns backbone probes each 6 kb total number of probes:
137207 gene probes (exon, intron, 5' and 3'-UTR): 69570 backbone
probes: 67637 probes (one each 6 kb on average).
13. The method according to claim 10, wherein said Device A for
Process A is a Comparative Genome Hybridization array.
14. The method according to claim 1, wherein Process B is carried
out with a Device B comprising a set of probes for said genes.
15. The method according to claim 14, wherein said set of probes
for said Device B comprises: probes of 70 to 120 pb, which
hybridize all the exons of said genes with at least 2.times. tiling
frequency.
16. The method according to claim 14, wherein said set of probes
for said Device B for Process B is prepared according to the
following rules: exonic regions apart from 3'UTR are covered,
exonic regions and intron-exon boundaries (200 bp upstream and
downstream of the exon) are covered, 1 kb upstream and downstream
of each gene (5' and 3' UTR) are covered, and probes are alternated
on (+) and (-) strands.
17. The method according to claim 1, characterized in that Process
B is carried out by a technique selected from the group consisting
of Sequence capture, on-chip capture and in-solution capture.
18. The method according to claim 17, characterized in that said
Device B is a Sequence capture array.
19. The method according to claim 1, characterized in that High
Throughput Sequencing is used in Process B.
Description
FIELD OF THE INVENTION
[0001] The present invention relates to an in vitro method, the
preparation and the application thereof, for determining Inherited
Neuromuscular Disorders, more rapidly with more accuracy and less
cost.
BACKGROUND OF THE INVENTION
[0002] Inherited Neuromuscular Disorders (hereafter NMDs) form a
large and very heterogeneous group of genetic diseases that cause
progressive degeneration of the muscles and/or motor nerves that
control movements. Most NMD types result in chronic long term
disability posing a significant burden to the patients, their
families and public health care. Life is usually shortened by
multiple and cumulative defects that occur during disease
progression. Premature death may result from cardiac and
respiratory muscle involvement. Namely pathologies such as Muscular
Dystrophies (hereafter MD), limb girdle muscular dystrophies
(hereafter LGMD), congenital muscular dystrophies (hereafter CMD),
and other neuromuscular diseases such as congenital myopathies
(hereafter CM) and Duchenne/Becker Muscular Dystrophies (DMD/BMD)
represent a large proportion of NMDs.
[0003] These pathologies are present in all populations, affecting
children as well as adults. The overall prevalence of NMDs is very
difficult to evaluate, but one can estimate that, given the
incidence of every different type, around 1 out of 1000 people may
have a disabling inherited neuromuscular disorder.
[0004] The precise determination of NMDs requires a conjunction of
extensive clinical examination and targeted complementary tests:
biological analyses, electromyography, imaging, and histological
analysis of biopsies. Numerous genes containing disease causing
mutations responsible for NMDs are known; thus molecular genetic
analyses are performed both to confirm the clinical diagnosis and
to precise the genotype of each patient. However, one cannot avoid
the difficulties in making a molecular determination of these
diseases, due to frequent overlaps of clinical phenotypes, the
large number of known genes, large genes that lack "hot spots" of
mutations, etc. . . . . As a consequence, according to reliable
estimate, 30 to 40% of patients remain devoid of genetic
confirmation of their disease type, although disease causing
mutation lies in an already known gene.
[0005] Most of the molecular approaches currently used for genetic
analysis correspond to gene by gene explorations, starting by the
most pertinent one.
[0006] As shown in FIG. 1, in the current state of the art
diagnostic process, in most cases, two kinds of samples are
necessary: muscle (and/or skin) biopsy sample and blood sample.
[0007] NMDs analysis is carried out on DNA extracted from blood
samples according to the following steps:
(1) a molecular analysis of the most pertinent gene 1 is
implemented, in order to identify abnormality on said gene 1; and
(2) if no abnormality is detected, after a clinical consultation, a
molecular analysis is implemented on the second most pertinent gene
2, in order to search a possible abnormality on said gene 2.
[0008] The above steps are repeated for pertinent genes in
decreasing order of pertinence, until a mutation is detected,
giving a genetic confirmation of disease, before turning to therapy
phase.
[0009] The total time necessary for finding the mutation can be up
to one year, or even more for some cases.
[0010] Thus with the presently available technologies, a
differential molecular genotyping is required, which is highly
complex and time consuming (some weeks to one year).
[0011] Many patients thus remain devoid of genetic confirmation of
their disease. To date, this proportion amounts to 30 to 40% of
patients suffering of NMDs. Importantly, new cutting edge
therapies, such as exon skipping, cannot be contemplated if no
precise genetic analysis is available.
[0012] Piluso et al. (1) disclose a comparative genomic
hybridization microarray for copy number variations in 245 genes
and 180 candidate genes implicated in NMDs.
[0013] Even though the method of Piluso et al. allows detecting
copy number variations, said method does not allow detecting all
the molecular causes of Inherited Neuromuscular Disorders.
[0014] It would therefore be desirable to provide a method for
determining all the molecular causes of Inherited Neuromuscular
Disorders more rapidly, with more accuracy and less cost.
SUMMARY OF THE INVENTION
[0015] The applicant has now found that such an aim is achieved by
a in vitro method of identifying molecular causes for at least one
of MD, LGMD, CMD and other neuromuscular diseases.
[0016] As used herein, "molecular causes" indicates mutations due
to Copy Number Variations (hereafter CNVs) and point mutations.
[0017] As used herein, "other neuromuscular diseases" indicate all
the neuromuscular diseases mentioned in the gene table of Kaplan
(2), other than MD, LGMD and CMD.
[0018] More precisely, the present invention relates to a method of
identifying in vitro molecular causes of Inherited Neuromuscular
Disorders, comprising the following steps:
(i) providing a physiological sample comprising a genome of a
subject, and (ii) implementing on said sample at least one of
Process A and Process B, wherein: [0019] Process A is determining a
number of copy number variation(s), with respect to a sample of a
normal subject, on at least 25 genes selected from the 31 genes of
Group 1 in Table 1 and [0020] Process B is determining a number of
point mutation(s) with respect to a sample of a normal subject on
at least 25 genes selected from the 31 genes of Group 1 in Table
1.
[0021] In order to detect at least one of MD, LGMD, CMD and other
neuromuscular diseases, it is mandatory to detect all different
mutations in the targeted genes.
[0022] Two types of gene mutations are involved in said NMDs:
[0023] 1. CNV, and [0024] 2. Point mutation.
[0025] As used herein, "Copy Number Variation (CNV)", is an
alteration of the DNA of a genome, resulting in an abnormal number
of copies of one or more sections of the DNA. CNV can be a gain or
a loss of specific DNA sequence(s) in DNA, such as deletions,
duplications or amplifications of sequence(s).
[0026] As used herein, "point mutation" is replacement of single
base nucleotide with another nucleotide of the genetic
material.
[0027] As used herein, "a normal subject" indicates a subject who
is devoid of any neuromuscular disease.
[0028] Process A allows determining a number of CNV(s) on at least
one of the targeted genes of Table 1, and thus determining a number
of at least one of MD, LGMD, CMD and other neuromuscular diseases
arising from CNV(s).
[0029] In one embodiment of a method of identifying in vitro
molecular causes of Inherited Neuromuscular Disorders of the
present invention, step (ii) comprises only Process A.
[0030] Process A however does not allow detecting (a) point
mutation(s) on said genes.
[0031] Process B allows detecting (a) point mutation(s) on said
genes of Table 1, and thus determining a number of at least one of
MD, LGMD, CMD and other neuromuscular diseases arising from (a)
point mutation(s).
[0032] In another embodiment of a method of identifying in vitro
molecular causes of Inherited Neuromuscular Disorders of the
present invention, step (ii) comprises only Process B.
[0033] Therefore, it is interesting to implement Process B in order
to detect (a) point mutation(s) on said genes, thus enabling to
determine a number of at least one of MD, LGMD, CMD and other
neuromuscular diseases with a higher rate of determination with
respect to a well known technique of the prior art and any
conventional technique.
[0034] Particularly, since Process A and Process B are
complementary, their combined use allows determining all possible
molecular causes on said genes with a high determination rate.
[0035] In a preferred embodiment of a method of identifying in
vitro molecular causes of Inherited Neuromuscular Disorders of the
present invention, step (ii) comprises Process A and Process B.
[0036] Table 1 hereafter presents 62 genes which have been
identified, after extensive research on NMDs, to be involved in at
least one of MD, LGMD, CMD and other neuromuscular diseases.
[0037] The definition of each gene can be found on
http://genome.ucsc.edu.
TABLE-US-00001 TABLE 1 ACTA1 BAG3 CFL2 CHKB ANO5 DAG1 DNAJB6 CNTN1
BIN1 LAMP2 FKTN ICSU CAPN3 LDB3 GDF8 ITGA7 CAV3 MTM1 KLH9 MYBPC3
COL6A1 MYH7 MYH2 PLEC1 COL6A2 NEB POMGNT1 TCAP COL6A3 PABPN1 SGCB
Group 4 DES PTRF SGCD DMD SYNE1 Group 3 DNM2 SYNE2 DOK7 TNNT1 DYSF
TPM2 EMD TPM3 FHL1 VCP FKRP Group 2 FLNC GNE KRYAB LAMA2 LARGE LMNA
MYOT POMT1 POMT2 RYR1 SEPN1 SGCG SGCA TRIM32 TTN Group 1
[0038] In Table 1, 31 genes are classified as Group 1 corresponding
to the highest level of implication, 15 genes are classified as
Group 2 corresponding to a higher level of implication, 9 genes are
classified as Group 3 corresponding to a high level of implication,
and 7 genes are classified as Group 4 corresponding to a certain
level of implication, in at least one of MD, LGMD, CMD and other
neuromuscular diseases
[0039] Table 2 shows the implication of the genes of Table 1 in
each disease.
TABLE-US-00002 TABLE 2 61 genes of Table 1 classified by
implications in each of NMDs Other neuro muscular MD LGMD CMD
diseases A B A B C A B C A B C DMD FHL1 CAV3 DNAJB6 TCAP LAMA2
POMGTN1 TCAP ACTA1 CFL2 ICSU EMD SYNE1 LMNA SGCB PLEC1 POMT1 FKTN
ITGA7 SEPN1 MTM1 LMNA SYNE2 MYOT SGCD POMT2 FHL1 CHKB TPM2 MYH2 GNE
PTRF CAPN3 POMT1 FKRP DMN2 MYBPC3 TPM3 KLH9 DOK7 DYSF POMT2 LARGE
MYOT CNTN1 NEB GDF8 ANO5 POMGNT1 COL6A1 KLH9 TRIM32 TNNT1 FHL1 SGCG
FKTN COL6A2 RYR1 FKRP COL6A3 MYH7 TTN SEPEN1 DNM2 TRIM32 TTN BIN1
DAG1 FLNC MTM1 SGCA LMNA VCP KRYAB DES FLNC MYOT LDB3 BAG3 LAMP2
PABPN1
[0040] In Table 2, the genes implicated in each disease are
classified according to their level of implication: the genes
classified as A correspond to the highest level of implication, the
genes classified as B correspond to a higher level of implication,
and the genes classified as C correspond to a high level of
implication.
DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0041] As shown in FIG. 2, providing a blood sample is sufficient
to implement the method of the present invention.
[0042] The present invention relates to a method of identifying in
vitro molecular causes of Inherited Neuromuscular Disorders,
comprising the following steps:
(i) providing a physiological sample comprising a genome of a
subject, and (ii) implementing on said sample at least one of
Process A and Process B, wherein: [0043] Process A is determining a
number of copy number variation(s), with respect to a sample of a
normal subject, on at least 25 genes selected from the 31 genes of
Group 1 in Table 1, and [0044] Process B is determining a number of
point mutation(s), with respect to a sample of a normal subject, on
at least 25 genes selected from the 31 genes of Group 1 in Table
1.
[0045] In one embodiment of a method of identifying in vitro
molecular causes of Inherited Neuromuscular Disorders of the
present invention, step (ii) comprises only Process A.
[0046] In another embodiment of a method of identifying in vitro
molecular causes of Inherited Neuromuscular Disorders of the
present invention, step (ii) comprises only Process B.
[0047] In a preferred embodiment of a method of identifying in
vitro molecular causes of Inherited Neuromuscular Disorders of the
present invention, step (ii) comprises both Processes A and B.
[0048] As used herein, "targeted genes" signifies the genes on
which Process A or Process B is, or Process A and Process B are
carried out.
[0049] Process A allows determining a number of CNV(s) on at least
25 genes selected from the 31 genes of Group 1 in Table 1.
[0050] Process B allows determining a number of point mutation(s)
on at least 25 genes selected from the 31 genes of Group 1 in Table
1.
[0051] When the number of targeted genes increases, the
determination rate of at least one of MD, LGMD, CMD and other
neuromuscular diseases is increased.
[0052] When step (ii) comprises both Process A and Process B, said
at least 25 genes of Group 1 for Process A and Process B can be
selected dependently of independently from said at least 25 genes
of Group 1 for Process B. In other terms, the genes used in Process
A and Process B may be the same or may be partly or totally
different from each other.
[0053] In one preferred embodiment, Process A or Process B is, or
Process A and Process B are carried out on all the 31 genes of
Group 1 in Table 1.
[0054] In a more preferred embodiment, Process A or Process B is,
or Process A and Process B are carried out on all the 31 genes of
Group 1, and on at least 10, preferably all the 15 genes of Group 2
in Table 1.
[0055] When step (ii) comprises both Process A and Process B, said
at least 10 genes of Group 2 for Process A and Process B can be
selected dependently or independently from said at least 10 genes
of Group 2 for Process B. f
[0056] In an even more preferred embodiment, Process A or Process B
is, or Process A and Process B are carried out on all the 31 genes
of Group 1, on all the 15 genes of Group 2, and on at least 5,
preferably all the 9 genes of Group 3 in Table 1.
[0057] When step (ii) comprises both Process A and Process B, said
at least 5 genes of Group 3 for Process A and Process B can be
selected dependently or independently from said at least 5 genes of
Group 3 for Process B.
[0058] In a most preferred embodiment, Process A or Process B is,
or Process A and Process B are carried out on all the 31 genes of
Group 1, on all the 15 genes of Group 2, on all the 9 genes of
Group 3, and on at least 4, preferably all the 7 genes of Group 4
in Table 1.
[0059] When step (ii) comprises both Process A and Process B, said
at least 4 genes of Group 4 for Process A and Process B can be
selected dependently or independently from said at least 4 genes of
Group 4 for Process B.
[0060] In another most preferred embodiment providing an excellent
rate of detection, Process A or Process B is, or Process A and
Process B are carried out on all the genes of the Table 3
hereunder:
TABLE-US-00003 TABLE 3 ACTA1 FKRP BAG3 DNAJB6 ANO5 FLNC DAG1 FKTN
BIN1 GNE LAMP2 MYH2 CAPN LAMA2 LDB3 SGCB CAV3 LARGE MTM1 SGCD
COL6A1 LMNA NEB CHKB COL6A2 MYOT PABPN1 CNTN1 COL6A3 POMT1 PTRF
ITGA7 DES POMT2 TNNT1 PLEC1 DMD RYR1 TPM2 TCAP DNM2 SGCG TPM3 DYSF
SGCA VCP FHL1 TTN CFL2
[0061] If one or more CNVs or one or more punctual mutations
are(is) detected, the physiological sample comprising a genome of a
subject is classified as positive and a precise type of at least
one of MD, LGMD, CMD and other neuromuscular diseases is allotted
to said sample.
[0062] Process A consists in [0063] providing a physiological
sample comprising a genome of a subject, and [0064] determining a
number of CNV(s) on targeted genes of the genome of the sample.
[0065] From the CNV(s) detected on said targeted genes, a person
skilled in the art can determine a number of at least one of MD,
LGMD, CMD and other neuromuscular diseases arising from CNV(s) on
said genes.
[0066] For example, if a CNV is detected on gene POMT1, which is
involved in both LGMD and CMD (c.f. Table 2), said sample has LGMD
or CMD arising from a CNV.
[0067] Here, Process A may be implemented by any well known
technique of the prior art and any conventional technique allowing
determining a number of CNV(s).
[0068] In one embodiment, Process A is carried out with a Device A
comprising a set of probes for said targeted genes.
[0069] In one particular embodiment, said Device A is a Comparative
Genomic Hybridization (CGH) array.
[0070] Therefore, for example, by using CGH technique, Process A
consists in [0071] providing a physiological sample comprising a
genome of a subject, [0072] providing a CGH array provided with a
set of probes for at least 25 genes selected from the 31 genes of
Group 1 in Table 1, [0073] analysing said sample using said CGH
array, and [0074] determining a number of CNV(s) in the DNA of the
sample.
[0075] A suitable physiological sample may be for example a biopsy
sample, whole blood, a lymphocyte culture, preferably, whole blood
or a lymphocyte culture, particularly preferably a lymphocyte
culture.
[0076] One usual blood sampling provides an amount of sample
sufficient for implementing the method of the present
invention.
[0077] As used herein, "Comparative Genomic Hybridization (CGH)" is
a type of nucleic acid hybridization assay which detects and
identifies the location of CNV. The technique is described in
detail, for example in references (3), (4) and (5).
[0078] CGH is a co-hybridization assay of differentially labelled
test DNA (for example green fluorescent dye) and reference DNA (for
example red fluorescent dye) that includes the following major
steps:
[0079] (1) immobilization of nucleic acids to a support to provide
an immobilized probe;
[0080] (2) pre-hybridization treatment to increase accessibility of
the probe and to reduce nonspecific binding;
[0081] (3) hybridization of a mixture of target nucleic acids to
the probe;
[0082] (4) post-hybridization washing to remove nucleic acid
fragments not hybridized to the probe; and [0083] (5) determination
of the target nucleic acids hybridized to the probes using a
determination device.
[0084] The 62 genes of Table 1 are involved in at least one of MD,
LGMD, CMD and other neuromuscular diseases.
[0085] Device A comprises a set of probes for at least 25 genes
selected from of the 31 genes of Group 1 on Table 1.
[0086] When the number of targeted genes increases, the
determination rate of at least one of MD, LGMD, CMD and other
neuromuscular diseases is increased.
[0087] Therefore in one preferred embodiment, said Device A
comprises a set of probes for the 31 genes of Group 1 in Table 1,
and for at least 10, preferably all the 15 genes of Group 2 in
Table 1.
[0088] In an even more preferred embodiment, said Device A
comprises a set of probes for all the 31 genes of Group 1, for all
the 15 genes of Group 2, and for at least 5, preferably all the 9
genes of Group 3 in Table 1.
[0089] In a most preferred embodiment, said Device A comprises a
set of probes for all the 31 genes of Group 1, for all the 15 genes
of Group 2, for all the 9 genes of Group 3, and for at least 4,
preferably all the 7 genes of Group 4 in Table 1.
[0090] CNV(s) in a tested DNA of the sample can be determined in
the following manner, using two colour labels:
[0091] In case of a deletion in the tested DNA, less tested DNA
will bind to the corresponding spots and a first colour label of
the reference DNA will prevail. Gains in the tested genome can be
identified by a dominance of second colour label of the tested DNA.
Spots representing sequences with the same copy number in the
tested genome relative to the reference genome are revealed by a
third colour.
[0092] Thus, the ratio fluorescence intensity of the tested
DNA/fluorescence intensity the reference DNA is then calculated, in
order to measure the copy number changes for a particular location
in the genome.
[0093] As used herein, "a set of probes" means a set of fragments
of nucleotides having sequences capable of hybridizing with the
sequence of the genes to be analysed.
[0094] A person skilled in the art can prepare a suitable set of
probes for said Device A, by any well known technique of the state
of the art, such as the method described by reference (6).
[0095] In one embodiment, said set of probes for said Device A
comprises: [0096] probes evenly spaced by about 50 bp distance
between two consecutive probes, which hybridize said gene plus a
region of about 2000 bp at the 5' and 3' terminal exons, and [0097]
backbone probes not evenly spaced by about 1000 bp distance between
two consecutive probes, which represent on average from 20 to 30%
of the total probes on said device.
[0098] As used herein, "evenly spaced" indicates "spaced by a same
interval".
[0099] As used herein, "backbone probes" are probes which hybridize
to locations on the genome going beyond the genes of interest, such
as intronic and potentially intergenic regions. They are used to
generate a calibration signal against which the test and reference
signals from the specific gene probes are measured.
[0100] As used herein, "covered" indicates "capable of hybridizing
with the sequence of the genes to be analysed".
[0101] In one particularly preferable embodiment, said set of
probes are manufactured according to the following rules:
[0102] probes cover gene+/-2 kb up and downstream,
[0103] average probe density is 1/50,
[0104] probes are alternated on (+) and (-) strands,
[0105] with a tiling of [0106] 10 pb tiling in exonic regions and
intron-exon boundaries (150 bp upstream and downstream of the exon)
[0107] 30 pb tiling in 3' and 5' UTR [0108] one probe for 100 bp in
introns
[0109] backbone probes each 6 kb,
[0110] total number of probes: 137207, [0111] gene probes (exon,
intron, 5' and 3'-UTR): 69570
[0112] backbone probes: 67637 probes (one each 6 kb on
average).
[0113] As used herein, "average probe density" indicates the
inverse of the mean distances between the start positions of
consecutive probe sequences on the indicated region of the
genome:
n - 1 i = 1 i = n - 1 [ ( [ distance ( Probe ] i , Probe i + 1 ) ]
) ##EQU00001##
where n is the number of probes in the considered region of the
genome.
[0114] As used herein, "tiling" indicates the mean distance between
consecutive probes. 1/Tiling represents the average probe
density.
[0115] This probe design allows increasing the robustness of the
determination of the present invention.
[0116] Process B consists in [0117] providing a physiological
sample comprising a genome of a subject, and [0118] determining a
number of point gene mutation(s) on targeted genes of the genomes
of the sample.
[0119] From said point mutation(s) detected on said targeted genes,
a person skilled in the art can determine a number of at least one
of MD, LGMD, CMD and other neuromuscular diseases arising from (a)
point mutation(s) on said genes.
[0120] For example, if a point mutation is detected on gene POMT1,
which is involved in both LGMD and CMD (c.f. Table 2), said sample
has LGMD or CMD arising from a point mutation.
[0121] Here, Process B may be implemented by any well known
technique of the prior art and any conventional technique allowing
determining a number of point mutation(s).
[0122] In one embodiment, Process B is carried out with a Device B
comprising a set of probes for said genes.
[0123] In one embodiment, Process B is carried out by a technique
selected from the group consisting of Sequence capture, "on-chip
capture" and "in-solution capture (Sure Select)".
[0124] In one particular embodiment, Device B is a Sequence capture
array.
[0125] Therefore, for example, Process B consists in [0126]
providing a physiological sample comprising a genome of a subject,
[0127] providing a sequence capture array provided with a set of
probes for at least 25 genes selected from the 31 genes of Group 1
on Table 1, [0128] analysing said sample using said sequence
capture array, and [0129] determining a number of punctual
mutation(s) in the DNA of the sample.
[0130] For Process B, the same physiological sample as that
prepared for Process A may be used.
[0131] The 62 genes of Table 1 are involved in at least one of MD,
LGMD, CMD and other neuromuscular diseases.
[0132] Said Device B comprises a set of probes for at least 25
genes selected from the 31 genes of Group 1 on Table 1.
[0133] When the number of targeted genes increases, the
determination rate of a number of at least one of MD, LGMD, CMD and
other neuromuscular diseases is increased.
[0134] In one preferred embodiment, said Device B comprises a set
of probes for the 31 genes of Group 1 in Table 1, and for at least
10, preferably all the 15 genes of Group 2 in Table 1.
[0135] In one more preferred embodiment, said Device B comprises a
set of probes for all the 31 genes of Group 1, for all the 15 genes
of Group 2, and for at least 5, preferably all the 9 genes of Group
3 in Table 1.
[0136] In one more preferred embodiment, said Device B comprises a
set of probes for all the 31 genes of Group 1, for all the 15 genes
of Group 2, for all the 9 genes of Group 3, and for at least 4,
preferably all the 7 genes of Group 4 in Table 1.
[0137] "DNA sequence capture" consists in isolating and sequencing
a genomic region of interest (targeted region), to the exclusion of
the remainder of the genome, and then sequencing the captured DNA
fragments.
[0138] "Sequencing" means determining the sequence of target DNA
fragments.
[0139] DNA sequence capture includes the following major steps:
[0140] (1) preparation of a sequencing library of test DNA;
[0141] (2) hybridization of said sequencing library to a support
with immobilized probes thereon;
[0142] (3) post-hybridization washing to remove nucleic acid
fragments not hybridized to the probe;
[0143] (4) target DNA fragment elution;
[0144] (5) PCR amplification of target DNA fragment; and
[0145] (6) sequencing of target DNA fragment.
[0146] In the present invention, the term "target regions"
indicates regions of a gene which are especially involved in at
least one of MD, LGMD, CMD and other neuromuscular diseases.
[0147] A person skilled in the art can manufacture a suitable set
of probes for said Device B by any well known technique of the
prior art and any conventional technique, such as the method
described by reference (6).
[0148] In one embodiment, said set of probes for said Device B
comprises:
[0149] probes of 70 to 120 bp, which hybridize all the exons of
said genes with at least 2.times. tiling frequency.
[0150] As used herein, "tiling frequency" indicates the density of
tiling. For example, 2.times. tiling frequency means that each base
is covered by two different probes.
[0151] In one embodiment, said set of probes for said Device B for
Process B is prepared according to the following rules:
[0152] exonic regions apart from 3'UTR are covered,
[0153] exonic regions and intron-exon boundaries (200 bp upstream
and down stream of the exon) are covered,
[0154] 1 kb upstream and downstream of each gene (5' and 3' UTR)
are covered, and
[0155] probes are alternated on (+) and (-) strands.
[0156] This probe design allows increasing the robustness of the
determination of the present invention.
[0157] Device B of the present invention preferably comprises an
array or solid particles suspended in liquid such as magnetic
particles.
[0158] In one embodiment, High Throughput Sequencing (hereafter
HTS) is used in Process B, for allowing further lowering the cost
of analysis.
[0159] Device A may be manufactures as follows:
[0160] The sequences of targeted genes known to be responsible for
at least one of MD, LGMD, CMD and other neuromuscular diseases were
obtained from the web site of the UCSC (http://genome.ucsc.edu),
and are shown in Table 1.
[0161] The genes on which analysis is implemented are selected from
Table 1, as explained above.
[0162] A set of probes for Device A can be designed by a well known
technique of the state of the art, as explained above.
[0163] For example, CGH arrays which may be used in Process A may
be manufactured by any manufacturer specialized in preparation of
such arrays, such as Roche-Nimblegen.
[0164] After completion of the preparation of a set of probes, the
probes may be fixed on the support to prepare a CGH array.
[0165] In one embodiment, a CGH array containing a set of probes
for all the 62 genes in Table 1 was prepared.
[0166] This approach is consistent with the chosen technology,
allowing the spot of up to 12.times.135 000 probes in the same
array, thus identifying at a glance deletions or duplications in
all the known genes with a high resolution (one probe every 10
bases or so).
[0167] Device B may be manufactured as follows:
[0168] Sequences of targeted genes known to be responsible for at
least one of MD, LGMD, CMD and other neuromuscular diseases were
obtained from the web site of the UCSC, and are shown in Table
1.
[0169] The genes on which analysis is implemented are selected from
Table 1, as explained above.
[0170] A set of probes for Device B is designed by a well known
technique of the state of the art, as explained above.
[0171] For example, sequence capture arrays which may be used in
Process B may be manufactured by any manufacturer specialized in
preparation of such arrays, such as Roche-Nimblegen or Agilent.
[0172] After completion of the preparation of a set of probes, the
probes may be fixed on the support to prepare a sequence capture
array.
[0173] In one preferred embodiment, a sequence capture array
containing a set of probes for all the 62 genes in Table 1 was
prepared.
[0174] This approach is consistent with the chosen technology,
allowing the spot of 1.times.385 000 probes in the same array. The
sequences captured by this array, are then desorbed and
characterized by HTS. Advantage of HTS is that, for example, 10
patients could be pooled and sequenced simultaneously decreasing by
10 the cost of mutation identification.
[0175] The methods according to the invention have advantageous
properties.
[0176] Process A allows determining a number of CNV(s) on at least
25 genes selected from the 31 genes of Group 1 in Table 1.
[0177] Process B allows determining a number of point mutation(s)
on at least 25 genes selected from the 31 genes of Group 1 in Table
1.
[0178] A combined determination of Process A and Process B allows
detecting all possible mutations on the targeted genes, and
therefore determining a number of at least one of MD, LGMD, CMD and
other neuromuscular diseases.
[0179] In particular, said combined determination allows increasing
the rate of determination of a number of at least one of MD, LGMD,
CMD and other neuromuscular diseases.
[0180] The present challenge lies in increasing determination rate
via characterisation of all mutation types, allowing
characterization of the genotype also in rare and atypical
phenotypes, in genetically ambiguous sporadic cases and in NMDs
whose pathophysiology is multiallelic or multigenic.
[0181] By a gene by gene approach analysis of the art of the
technique, from 30% to 40% of patients suffering from NMDs are
devoid of genetic confirmation. In contrast, by the analytic method
of the present invention, the rate of non-analysed patients is
usually less than 5%, when Process A and Process B are carried out
on 62 genes.
[0182] Because of the special selection of the group of genes of
Table 1, involved in at least one of MD, LGMD, CMD and other
neuromuscular diseases, and of the specific Devices A and B both
provided with a set of probes for said group of genes, the process
of the present invention allows determining all possible mutations
in said genes and therefore determining a number of at least one of
MD, LGMD, CMD and other neuromuscular diseases, with a rate of
determination of at least 90%, often at least 95%, and generally at
least 99%, when Process A and Process B are carried out on all the
62 genes of Table 1.
[0183] A further subject matter of the present invention relates to
a method for determining at least one of MD, LGMD, CMD and other
neuromuscular diseases, comprising implementing the above mentioned
step(s) of determination.
[0184] The method of the present invention can be applied to the
determination of a number of CNV(s) or point mutation(s), or CNV(s)
and point mutation(s) arising from at least one of MD, LGMD, CMD
and other neuromuscular diseases.
[0185] In one embodiment of a method of identifying in vitro
molecular causes of Inherited Neuromuscular Disorders of the
present invention, step (ii) comprises only Process A.
[0186] In another embodiment of a method of identifying in vitro
molecular causes of Inherited Neuromuscular Disorders of the
present invention, step (ii) comprises only Process B.
[0187] In a preferred embodiment of a method of identifying in
vitro molecular causes of Inherited Neuromuscular Disorders of the
present invention, step (ii) comprises both Process A and Process
B.
[0188] If one or more CNVs or one or more punctual mutations
are(is) detected, the physiological sample comprising a genome of a
subject is classified as positive and a precise type of at least
one of MD, LGMD, CMD and other neuromuscular diseases is allotted
to said sample.
[0189] The present invention provides sensitive and reliable tools
for detecting at least one of MD, LGMD, CMD and other neuromuscular
diseases with a high determination rate, as evidenced by the
Examples.
[0190] Said determination rate is at least 90%, often at least 95%,
and generally at least 99%.
[0191] With the genes of Table 3, the determination rate is at
least 99%, and almost 100% in patients with NMDs whose prevalence
is greater than or equal to 1/100000.
[0192] They allow determining all possible mutation(s) involved in
at least one of MD, LGMD, CMD and other neuromuscular diseases, in
targeted gene(s) in only a single step process (2,100,000
probes).
[0193] This is possible due to the specificity of the selection of
the group of genes of Table 1, involved in at least one of MD,
LGMD, CMD and other neuromuscular diseases, and the specificity of
Device A and Device B, both provided with a set of probes for said
groups of genes, with a high determination rate. Said determination
rate is at least 90%, often at least 95%, and generally at least
99%, when Process A and Process B are carried out on all the 62
genes of Table 1.
[0194] The process of the present invention increases the ratio of
precisely analysed patients (either new analysed patients or
reoriented patients for which initial analysis was erroneous).
[0195] Therefore the process of the present invention allows
improving genetic counseling and patient management, establishing
phenotype-genotype correlations, constructing dedicated databases
and including patients in current or future clinical trials due to
the special selection of groups of genes to be analysed.
[0196] The present invention allows also reducing analysis costs by
the special selection of group of genes to be analysed, and by
using platforms with high analytic capacities. The method of the
present invention really corresponds to a "one-shot" technology
that considerably reduces both the time and the cost of the whole
analytic process.
[0197] Such an approach also dramatically reduces the costs
associated to analysis on the medium term. On the long term this
contributes to decreasing the global prevalence of NMDs by
developing a suitable analytic counseling.
[0198] The special selection of groups of genes to be analysed
allows reducing the time-to-analysis (down to 72 h to one week) for
patients and families.
[0199] One must keep in mind that patients with a well
characterized pathology, both on clinical and genetic sides, are
the only one eligible for clinical trials or protocols, which
become more and more numerous.
[0200] The scope of the invention can be understood better by
referring to the examples given below, the aim of which is to
explain the advantages of the invention. The invention will now be
described by means of the following Examples.
DESCRIPTION OF THE DRAWINGS
[0201] FIG. 1 shows a flow chart depicting the major steps involved
in detecting at least one of MD, LGMD, CMD and other neuromuscular
diseases, using the gene by gene exploration of the prior art.
[0202] FIG. 2 shows a flow chart depicting the major steps involved
in detecting at least one of MD, LGMD, CMD and other neuromuscular
diseases using a method of the present invention.
[0203] FIG. 3 shows the result of analysis of a sample taken from
one uncharacterized male LGMD patient, using a CGH array.
[0204] FIG. 4 shows the result of analysis of a sample taken from
one uncharacterized female LGMD patient, using a CGH array.
[0205] FIGS. 5 and 6 show the result of analysis of DNA from 2
patients, using CGH array showing new candidates genes for
LGMD.
[0206] FIG. 7 shows the results of identification of a genomic
variation in a patient using sequence capture and Illumina
sequencing.
EXAMPLES
Example 1
Manufacture of Devices
[0207] A CGH array and a sequence capture array ware prepared by
Digital Mirror Device according to methods known in the art. The
Digital Mirror Device creates "virtual masks" that replace physical
chromium masks used in traditional arrays.
[0208] These "virtual masks" reflect the desired pattern of UV
light with individually addressable aluminium mirrors controlled by
the computer. The DMD controls the pattern of UV light projected on
the microscope slide in the reaction chamber, which is coupled to
the DNA synthesizer. The UV light selectively cleaves a UV-labile
protecting group at the precise location where the next nucleotide
will be coupled. The patterns are coordinated with the DNA
synthesis chemistry in a parallel, combinatorial manner such that
385,000 to 4.2 million unique probe features are synthesized in a
single array.
[0209] The set of probes for CGH array has been selected according
to the following rules:
[0210] probes cover gene+/-2 kb
[0211] average probe density is 1/50
[0212] probes are alternated on (+) and (-) strands
[0213] with a tiling of [0214] 10 pb tiling in exonic regions and
intron-exon boundaries (150 bp upstream and downstream of the exon)
[0215] 30 pb tiling in 3' and 5' UTR [0216] one probe for 100 bp in
introns
[0217] backbone probes each 6 kb
[0218] total number of probes: 137207 [0219] gene probes (exon,
intron, 5' and 3'-UTR): 69570 [0220] backbone probes: 67637 probes
(one each 6 kb on average). [0221] The set of probes for sequence
capture array has been selected according to the following
rules:
[0222] exonique regions apart from 3'UTR are covered,
[0223] exonic regions and intron-exon boundaries (200 bp upstream
and downstream of the exon) are covered,
[0224] 1 kb upstream and downstream of each gene (5' and 3' UTR)
are covered, and
[0225] probes are alternated on (+) and (-) strands.
Example 2
CGH Array NimbleGen
Starting Material:
[0226] Genomic DNA from patients is used as starting material for
CGH analysis. It will be compared to a reference DNA corresponding
to a pool of anonymous donors (Promega, G1521).
[0227] The extraction protocol recommended for DNA purification is
the Qiagen DNeasy Blood & Tissue Kit. (Qiagen, 50x, cat. no.
69504). Optional RNase treatment step must be achieved for these
applications (RNase A, 100 mg/ml, cat. no. 19101).
Quality Control:
[0228] DNA are assessed for quality and concentration using
respectively agarose gel and spectrophotometer method (Nanodrop,
ND-1000). RNase A treatment is recommended as RNA contamination
could interfere during hybridization.
[0229] The quality control of genomic DNA is based on Nanodrop
spectrophotometer measurements. Absorbance at 260 nm (A260) is used
to assess quantity and A260/A280, A260/A230 ratios are calculated
to assess purity of samples.
[0230] These ratios should be as follows: A260/A230.gtoreq.1.9
[0231] A260/A280.gtoreq.1.8
[0232] To determine integrity of DNA, 250 ng should be analyzed on
a 1% agarose gel to ensure that they show no sign of RNA
contamination or degradation.
DNA Labelling:
[0233] Each genomic DNA from patients is labelled using known
fragment allowing incorporating cyanin 3 (Cy3) in the DNA. In the
same time, reference DNA is labelled using the same method except
that cyanin 5 (Cy5) is incorporated instead of Cy3.
Hybridization:
[0234] Same quantity of labeled DNA is then pooled (1 DNA from
patient with the reference DNA) in a suitable hybridization
cocktail and added into a hermetic chamber on the array.
Hybridization is led during 3 days at 42.degree. C. using the
NimbleGen hybridization Station.
Washing and Scanning:
[0235] Arrays are washed using several buffers by increasing
stringency and finally dried. Slides are then scanned twice in a 2
.mu.m-resolution scanner (MS200 NimbleGen) using 2 wave-lines
corresponding to each fluorochrome.
Data Analysis:
[0236] Quality control check and grid alignment are performed on
scanned images. NimbleScan software is then used to convert
intensity into raw data files and calculate log 2 (ratio)
corresponding DNA from patients normalized by the reference. Ratio
data are in .gff format file allowing visualizing the results using
a genome browser (SignalMap) or other third part tools (like
CGH-web).
[0237] For a detailed protocol see:
http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf
2-1: Deletions in DMD (Process A)
[0238] A blood sample was taken from one male patient supposed to
be suffering of LGMD. This sample was analysed with a CGH array
provided with a set of probes for the 62 genes of Table 1.
[0239] As shown in the signal map visualization of FIG. 3, a
hemizygous deletion of exons 45 to 47, genomic size: 173.020 bp was
detected in the sample.
[0240] In FIG. 3, the abscissa indicates genomic coordinates, and
the ordinate indicates the log 2 ratio of signals.
[0241] The breakpoints determined by CGH are ChrX:
31827185-32000205. The deletion by qPCR and delimited the
breakpoints in a 2 kb interval was confirmed (chrX:
31827185-2000-32000205+774).
[0242] The deletion results in an in-frame deletion:
c.6439.sub.--6912del (p.Glu2147-Lys2304del).
[0243] This result indicates that the male patient supposed to be
suffering of LGMD is in fact attained by DMD.
2-2: Deletions in DMD (Process A)
[0244] A blood sample was taken from one female patient supposed to
be suffering of LGMD. This sample was analysed with a CGH array
provided with a set of probes for the 62 genes of Table 1.
[0245] A heterozygous deletion of exons 3 to 18 genomic size:
346.847 bp was detected in the sample (FIG. 4).
[0246] In FIG. 4, the abscissa indicates genomic coordinates, and
the ordinate indicates the log 2 ratio of signals.
[0247] The breakpoints determined by CGH are ChrX:
32432158-32779005. The deletion was confirmed by qPCR and delimited
the breakpoints in a 1 kb interval (ChrX:
32432158(-1276)-32779005(-365). The deletion results in an in-frame
deletion in the protein: c.94.sub.--2292del.
[0248] This result indicates that the non-analysed patient is in
fact attained by DMD.
2-3: Potential MD Genes: C6orf142 Process A
[0249] A blood sample was taken from 4 patients supposed to be
suffering of LGMD. These samples were analysed with a CGH array
provided with a set of probes for the 62 genes of Table 1 plus some
additional candidate genes for LGMD.
[0250] A homozygous deletion of around 30 kb (position around
54,210,000 to 54,540,000 of chromosome 6) was detected in one of
the patients (FIG. 5, third line) containing 2 coding exons (exon 9
and 10) of C6orf142 gene. We can also notice the detection of a
highly polymorphic CNV of less that 10 kb (position around
54,035,000 to 54,040,000) which illustrates the sensitivity of the
method.
[0251] In FIG. 5, the abscissa indicates genomic coordinates, and
the ordinate indicates the log 2 ratio of signals.
[0252] This 30 kb deletion is a potential mutation possibly
responsible of LGMD in this patient. If this result is validated,
C6orf142 would become a new gene involved in LGMD.
2-4: Potential MD genes: Cytoplasmic linker protein (CLIP)-170
(Process A)
[0253] A blood sample was taken from 2 patients supposed to be
suffering of LGMD. These samples were analysed with a CGH array
provided with a set of probes for the 62 genes of Table 1 plus
additional candidate genes for LGMD.
[0254] A 6-kb amplification was detected in the sample in line 1
(FIG. 6) in a region containing several coding exons (chromosome
12, around position 121,320,000 to 121,325,000).
[0255] In FIG. 6, the abscisa indicates genomic coordinates, and
the ordinate indicates the log 2 ratio of signals.
[0256] Amplification of this region has been validated by qPCR
indicated 2 additional copies in the patient genome. This variation
in copy number in CLIP gene is a possible mutation that could be
the genetic cause of LGMD in this patient.
Example 3
Sequence Capture Array (Process B)
[0257] In order to focus the sequencing on regions of interest,
sequence capture strategies have been developed. In this aim,
Agilent and Nimblegen propose in-solution capture methods that use
specific oligonucleotide probes targeting regions of interest.
These probes libraries are used to selectively capture DNA
fragments from patients corresponding to these regions addressed by
the sequencing. Here, next-generation sequencer HiSeq2000 from
Illumina is used.
Agilent Protocol:
[0258] (SureSelect Target Enrichment Kit, Agilent)
Quality Control:
[0259] DNAs are assessed for quality and concentration using
respectively agarose gel and spectrophotometer method (Nanodrop,
ND-1000). RNase A treatment is recommended as RNA contamination
could interfere during hybridization.
[0260] The quality control of genomic DNA is based on Nanodrop
spectrophotometer measurements. Absorbance at 260 nm (A260) was
used to assess quantity and A260/A280, A260/A230 ratios were
calculated to assess purity of samples.
[0261] These ratios should be as follows: A260/A230.gtoreq.1.9
[0262] A260/A280.gtoreq.1.8
[0263] To determine integrity of DNA, 250 ng was analyzed on a 1%
agarose gel to ensure that they show no sign of RNA contamination
or degradation.
DNA Preparation:
[0264] Genomic DNAs from patients were fragmented using Covaris
device to obtain fragments between 150 and 200 bp length. Then,
DNAs were repaired in order to get blunt-ended fragments that will
be subjected to an addition of 5'-Phosphate before an 3'-end
adenylation step. These modifications allow ligating specific
adaptors (TruSeq adaptors, Illumina) that will be used during the
sequencing step. To obtain enough material for the hybridization
step, a PCR amplification using Herculase II Fusion DNA Polymerase
(Ozyme) was performed.
[0265] The extraction protocol recommended for DNA purification is
the Qiagen DNeasy Blood & Tissue Kit. (Qiagen, 50x, cat. no.
69504). Optional RNase treatment step must be achieved for these
applications (RNase A, 100 mg/ml, cat. no. 19101).
Hybridization on in-Solution Library Probes:
[0266] DNA fragments were then hybridized 24 h at 65.degree. C. in
presence of the capture probes.
Purification of Captured DNA:
[0267] Magnetic beads selection allows discarding non specific DNA
and eluting the DNA fragments of interest. At the end of this step,
a PCR amplification step was performed in order to amplify the
material and to incorporate the specific TruSeq index sequences
(Illumina). This barcode system will allow pooling DNA from
different patients and sequencing all of them in a single
sequencing run.
Quantity Assessment:
[0268] Quantification was performed using qPCR kit (NGS Library
Quantification, Agilent) in order to pool the samples in equimolar
quantity. The pool was then ready for sequencing on HiSeq2000
platform.
[0269] For a detailed protocol see:
http://www.chem.agilent.com/Library/usermanuals/Public/G7530-90000_SureSe-
lect_IlluminaXTMultiplexed_v.1.2.pdf
NimbleGen Protocol: (SeqEZ Library, NimbleGen)
[0270] Protocol is very similar to Agilent SureSelect except for
the following few points:
[0271] Fragmentation must be between 200 and 400 bp length.
[0272] The TruSeq indexes are added before hybridization by
ligation.
[0273] Amplification is done using Fusion HF PCR master mix
(Ozyme).
[0274] Hybridization is performed at 47.degree. C. for 72 h.
[0275] Enrichment is assessed using qPCR methods to validate
capture efficiency.
[0276] For a detailed protocol see:
http://www.nimblegen.com/products/lit/06588786001_SeqCapEZLibrarySR_Gui
de_v3p0.pdf
3-1. Identification of a Genomic Variation (Process B)
[0277] FIG. 7 shows the result of identification of a genomic
variation in a patient using sequence capture and Illumina
sequencing. Several reads from the sequencing of one patient (blue)
have been aligned on the reference genome sequence (green). A
variant heterozygous position has been identified (red) where a G
allele is found in addition to the C corresponding to the reference
sequence.
3-2. Sequencing (Process B)
[0278] Table 4 shows the results of a sequencing run led on
Illumina HiSeq device using 2 DNA controls with known mutations
(CTR-1 and CTR-2) and 8 LGMD patients with unknown mutations.
TABLE-US-00004 TABLE 4 Results of a sequencing run led on Illumina
HiSeq device using 2 DNA controls with known mutations (CTR-1 and
CTR-2) and 8 LGMD patients with unknown mutation Sample Mutation
typeannot Gene chrom Ref CTR-1 SNP Nonsense DMD chrX G CTR-2 Indel
Deletion SGCA Chr17 C CTR-2 SNP Missense SGCA Chr17 G LGMD-1 SNP
Missence TTN Chr2 T LGMD-1 SNP Missence + TTN Chr2 C splice exon
LGMD-2 SNP Nonsense TTN Chr2 A LGMD-2 SNP Missense TTN Chr2 G
LGMD-3 SNP Missense CAPN3 Chr15 A LGMD-4 SNP Missense NEB Chr2 C
LGMD-4 SNP Missense NEB Chr2 C LGMD-5 Indel Deletion DYSF Chr2 G
LGMD-6 SNP Missense TTN Chr2 C LGMD-6 Indel Deletion TTN Chr2
TTTCCTCTTCAGGAGCAA LGMD-7 Indel Insertion ANO5 Chr11 -- LGMD-7 SNP
Missense ANO5 Chr11 A LGMD-8 SNP Nonsense ANO5 Chr11 C LGMD-8 Indel
Insertion ANO5 Chr11 -- Results of a sequencing run led on Illumina
HiSeq device using 2 DNA controls with known mutations (CTR-1 and
CTR-2) and 8 LGMD patients with unknown mutation Sample Variant
statut AA changes Polyphen CTR-1 A Het Q > STOP -- CTR-2 -- Het
Frameshift (1D) -- CTR-2 A Het V -> M Probably damaging LGMD-1 A
Het D -> V Probably damaging LGMD-1 T Het V -> M Probably
damaging LGMD-2 T Hom Y -> STOP -- LGMD-2 A Hom R -> C
Probably damaging LGMD-3 G Het Y -> C Probably damaging LGMD-4 T
Het G -> D Probably damaging LGMD-4 T het R -> Q Probably
damaging LGMD-5 -- Het Frameshift (1D) -- LGMD-6 T Het R -> H
Probably damaging LGMD-6 -- Het Deletion (18D) -- LGMD-7 A Het
Frameshift (1I) LGMD-7 G Het N -> S - probably damaging LGMD-8 T
Het R -> STOP -- LGMD-8 GGAC het Frameshift (4I) --
[0279] The 3 known mutations in both controls DNA have been easily
detected (stop codon in DMD gene for CTR-1 and 1 deletion and 1
pathogenic amino-acid substitution in SGCA gene for CTR-2).
Concerning the 8 patients with no mutation described so far, 3 of
them show mutations in TTN, 2 in ANO5, 1 in DYSF, CAPN3 and NEB.
All these genes belong to the core list of 62 genes of interest as
described in tables 1 and 2. These results illustrate the
efficiency of the tool and the strength of the process B to
identify point mutations.
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Sequence CWU 1
1
4118DNAHomo sapiens 1tttcctcttc aggagcaa 18225DNAHomo sapiens
2tgggctgagg agactgagca gggca 25325DNAHomo sapiens 3tgggctgagg
agagtgagca gggca 25426DNAHomo sapiens 4tgggctgagg gagactgagc agggca
26
* * * * *
References